Chih-Ying Lin wrote:
Hi
For one molecule, will Gromacs give the same set of force field
parameters to this molecule no matter this molecule is put in water or
in vacuum?
The bond length, the bond angle, and the dihedral angles of the same
molecule will be different in water and in vacuum.
So, will the force field parameters be changed/ adjusted in water than
in vacuum?
Assignment of force field parameters happens (e.g. by hand or with
pdb2gmx) before it is possible to verify whether a solvent or vacuum
simulation is intended. So you could do whatever you want and GROMACS
isn't going to change things on you or prevent you from doing things...
but probably most of these things aren't sensible. See
http://wiki.gromacs.org/index.php/Force_Fields
You should pick a force field that is known to work for the kind of
calculation you want to do.
How does Gromacs set the force field parameters for the molecule?
In pdb2gmx, atoms in residues have their names matched to a database of
residues (.rtp files), which then looks up the interactions in yet
another database (.atp and .itp files).
I mean..... are the force field paramters determined in local or in global?
I don't know what you mean.
Could I change parts of the force field parameters which I found from
the published paper?
Yes, but this would be a very bad idea for someone starting their MD
experience. See http://wiki.gromacs.org/index.php/Parameterization
Or, I could not change parts of the force field parameters; instead, I
have to change the whole set of the force field
parameters???
Read carefully and choose something appropriate in advance, so that
"changing" doesn't arise.
Mark
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